Fighting Fate, Fighting Extremis
by StarksViolet
Summary: Tony Stark made a definitive choice and now he had to live with it...however long that may be
1. Chapter 1

_**Wow it feels good to be back! It's been far too long and I've missed you all!**_

 ** _All the usual disclaimers of course, I don't own any characters etc...but I do love to borrow them from time to time._**

 ** _So this piece is once again based on The Extremis...only because it's still, to this day, my favorite of the Iron Man comics. So it's a little mix of the few Iron Man comics I've read recently, most recent being The Dark Reign series._**

 ** _Let me know how you all find it, and please be gentle, haven't been back for a long time :P_**

* * *

Tony Stark sucked in a deep breath and looked at the woman standing before him.

Her crystal eyes glistened with unshed tears as she looked at him silently, patiently, waiting for anything but the lie which he was about to tell.

'I'm ok,' he murmured taking her hands into his.

Pepper knew he was lying but she nodded just the same willing herself to believe it because what else did she have?

'I'll be home soon,' he added planting a kiss on her forehead, 'don't wait up.'

And with that he assembled the suit around himself and took off through the window leading up and outside into the cold, dark night leaving Pepper to her thoughts.

'Jarvis?' Pepper called with a heavy heart, she sat down on the edge of their bed and averted her gaze from the tiny droplets of crimson which she had definitely noticed.

'Yes Miss Potts.' He replied as he always had.

She swallowed hard and looked down at the floor, 'is…is Tony ok?'

The reply didn't come quickly and that was almost all she needed, she knew Jarvis wouldn't say anything Tony had instructed him not to.

'Mr Stark is currently experiencing some complications, but he is on the road to recovery.' Jarvis finally said.

'Thank you,' she breathed still unconvinced.

* * *

 **Two Days Later**

'I know you think that taking this virus was a good idea, but Tony, it really wasn't,' she all but shouted.

Tony stood maybe four or five feet away from her but she could still make out the dark circles under his eyes and the red rims surrounding his irises.

'You saw what it did to me Tony, you saw the pain and instability, what were you thinking?' Now she _was_ shouting and Tony stood back at a safe distance.

He didn't need to be a genius to know that the instability of the virus was the deadliest part and that the warmth slowly building under his skin and creeping in through his eyes was a warning sign. But he was a genius and now even more so.

Everything was heightened, beyond his comprehension, almost to a point where he himself didn't understand what he was going through, what he was capable of.

He swallowed hard and took a step toward her.

'You need to trust me,' he began softly to which Pepper replied by angrily slapping him.

'Don't you dare,' she hissed, 'you did the one thing that you know almost killed me, killed us!'

Damn. She was right. One point to Pepper.

'I needed to,' he simply said.

Pepper almost choked on a cough, 'seriously?'

He remained silent. He knew when he needed to keep his mouth shut.

'That's all you've got, seriously?' She shrieked, 'because you _needed_ to, why Tony, to be smarter, better? Why?'

'Pep please….' He tried to take her hand into his to no avail.

She was definitely pissed. Shit.

'You are insane,' she finally bit stepping away from him.

The red glow burning deep within his eyes, somewhere deep in the darkness of his core, was so unfamiliar it frightened her. _He_ frightened her.

He quickly looked away and muttered an almost inaudible apology before turning away and leaving her in almost a single stride.

* * *

 **Later that day**

Pepper leaned on the edge of her desk and looked across the room at Maria Hill. The two women, at the present time were responsible for running two of the most important organizations in the world headed by the most brilliant man in the world. At this present time both Maria Hill and Pepper Potts were completely and utterly devoted to representing the best interests of Tony Stark.

'Did you know?' Pepper asked finally, knowing without any doubt she had much more clearance over Hill than she did of her, especially when it came to Tony and Stark Industries.

Before she replied she looked at her with the same fierceness in her eyes. 'Yes, I did.'

'And you thought it best to hide this why?' Pepper asked suddenly not caring about formalities.

'Because he requested it be kept that way,' she replied.

'Even if it meant going against your _job_ to keep him safe?' Pepper asked incredulously.

This time Hill stepped toward her, 'yes, because _now_ he is safe.'

Pepper stood her ground and thought about the words which just came out of her mouth.

'What do you mean "now" he's safe?' She narrowed her eyes.

'That is something I can't discuss, I'm sorry Miss Potts.' She added finally, 'excuse me, I have work to do.'

'Maria,' Pepper called, quickly getting to her feet, 'please.'

A moment of silence fell between the women and the energy in the room shifted dramatically. No longer was Pepper the angry CEO and Hill the defensive Agent of SHIELD, they were both just women looking after the same man, on two completely different levels.

'Please, I need to know, what's happening to him?' Pepper asked so quietly she surprised herself, she'd never been one to plead to anyone, but this was different. This was about Tony and he always managed to bring out _this_ Pepper Potts. He always had that effect.

'Pepper…' Maria turned to look back at her, 'I can't.'

'You can, please,' she whispered, 'this affects both of us.'

'I'm not sure how he'd-'

Pepper cut her off, 'if anything happened to him and I didn't know about it, Maria, I don't know how I'd be able to fix that, I need to know if there's anything affecting him which could affect the company.' That was a low blow. She hated herself for making this out to be the sole reason she wanted to know Tony's deepest secret.

Maria stood with her arms folded tightly across her chest, watching and reading Pepper and her demeanour. She was one of the best Agents SHIELD had to offer and a lot of that now was used to run SHIELD under Stark's lead. She knew she would be betraying him, but the other side to that coin was that if she didn't tell, she would be betraying her job to protect his best interests, and his best interests were his health, his company and Pepper. And Pepper needed to know.

'You should sit down.' She said to Pepper doing the same.

A quick nod was all Pepper replied with as she sat down in her chair and motioned for Hill to speak.

'Tony didn't take the Extremis because he wanted to,' she began, already feeling guilty for doing this. 'He took it because he _needed_ to, you have to understand that before I continue.'

Pepper looked on quizzically but nodded.

'A few months ago, after the threat to you was neutralised we kept the virus in a safe location as requested by Tony, he knew that destroying it would be a mistake as would keeping it. So he neutralised it, de-weaponized it and stored it.'

Dozens of scenarios raced through Pepper's head, why would he need the Extremis, what on earth would he possibly use it for? She knew he wouldn't use it as a weapon, they were done with that. He said so himself, after Afghanistan after Iron Man, all of that had changed. So why would he keep it?

'At first he didn't want anything to do with it, especially after what Maya and Killian did to you, but he decided he needed it, he wanted to work on it, extract the regenerative sequencing it provided and fix himself…' Hill paused waiting for Pepper to catch up.

'Go on.' Pepper nodded.

'So he found a way to implement the healing properties enough so that it would allow him a safe way to remove the arc reactor.'

'That's why he was able to remove it, after so many years…' Pepper whispered to herself, finally piecing everything together in her head.

Hill nodded and got up, she began to pace around the office looking out across the crystalline blue skies.

'A few weeks after that we got word that someone else, someone more dangerous had access to the same virus and was activated after Maya and all of her research was destroyed,' she paused to look at Pepper who had turned two shades whiter than what she usually was.

'He was another soldier, Rick Snow, another experiment…' she trailed off looking at Pepper.

'Needless to say we were unprepared,' Hill choked back a sarcastic laugh, 'hilariously unprepared.'

Pepper swallowed hard and looked on waiting for her to finish, suddenly not certain she wanted to know what she was telling her.

'The reports were alarming, soon we knew enough to track him, once we did we were faced with a decision, go in and probably die but stop him, or wait and let Snow destroy half the city. Tony decided then and there that we couldn't risk any more lives, so he, Natasha and Steve went in, again, we were completely unprepared.'

Hill stopped and closed her eyes recalling the images of that day.

'Tony ordered them out, pretty much had them forcefully removed by the Iron Legion and he stayed taking him on,' she opened her eyes and let out a sigh. 'He was successful, he killed Snow and stopped the threat, but not without a huge sacrifice.'

'What happened?' Pepper whispered almost wishing she didn't.

'Snow was strong, he did a lot of damage to the suit and to Tony, once we finally got released from his Iron Legion we weren't prepared for what we saw, he was hanging on to life by a thread, Jarvis had of course medicated him with morphine as soon as it happened but the extent of the damage wasn't known until we flew him back to base.'

Pepper's heart was racing and through tears she motioned for Hill to go on.

'Snow had broken Tony's back, shattered his spine in four separate locations as well as his right arm and leg, the doctors told us that _if_ he made it, he would be paralysed from the chest down, if the damage didn't spread during the surgery.'

A shaky sigh left Pepper's lips to which she quickly responded by covering her mouth with her hands, as if that would stop the emotions from pouring out.

Hill sat down and looked Pepper in the eyes, 'he pulled through, barely,' she shook her head looking away, 'he refused to speak to any of us, not even the doctors, so I did the only thing I knew, I gave him work, research, anything to get his mind off what had happened.'

'You gave him the Extremis…' Pepper knew the answer without Hill needing to say anything at all.

She nodded, 'I hoped that he would be able to do what he had done with the reactor, mend it, or at least if nothing more, his mind would be off…everything else.'

Pepper quietly got to her feet and walked across the room to the window and just took the world in. All that beauty on the surface with all those ignorant people living their lives down on the streets below. Did they even know the darkness which bubbled just beneath the surface?

She did. She saw the darkness and experienced it every time Tony came home bloodied and bruised with pain and sorrow looming behind his dark brown eyes.

She turned to look at Hill.

'At what cost?' She finally asked.

Hill looked down at her hands in response, 'I don't know.'

'Thank you,' Pepper murmured deciding that she had no energy left to hear any more. Her heart was heavy and darkness was on the forefront on her mind.

She poised herself and quietly made her way into elevator and down to the ground floor. 'Oh Tony,' she shook her head looking up to the skies.

* * *

 **The Next Day**

Tony walked into the work shop slightly limping, slightly dragging his left leg all whilst trying desperately to ignore the pulsing headache which raged in his skull and the chastising look Pepper was throwing his way. He threw down the malfunctioning gauntlets and winced as the loud crashing sound irritated his already bad headache.

'J, scans, now.' He hissed dropping less than gracefully into his work chair.

Pepper kept a cautious distance, silently watching trying to work out the extent of his injuries and if she could notice any difference in him, in the Extremis. Nothing. He looked normal and definitely acted normal.

'Sir, it seems that you have sustained a hair line fracture to the left ankle, preliminary scans are promising, the Extremis is rapidly repairing the damage.' Jarvis announced.

Tony glanced up at pepper before popping off the top of his canteen and taking a swig of chlorophyll, 'not rapidly enough.' He muttered.

'This is still much faster than if you were to heal on your own,' Jarvis explained to which Tony rolled his eyes and nodded.

'Don't look at me like that, Pep.' He said without making eye contact.

Pepper sighed and slowly made her way over to him eager to see for herself that the damage wasn't severe, slowly she knelt down before him and gingerly lifted the cuff of his pants and examined the violent bruises splashing against his creamy skin.

'I'll get an ice-pack,' she said getting to her feet.

'It's ok,' he replied taking hold of her hand, 'I'm ok, see,' he gingerly applied pressure on the injured foot with no apparent pain.

Pepper shook her head taking her hand back and instead placing it on her hip.

A few moments later Tony got up and stepped toward her, closing the gap between them.

'I know you don't like this,' he whispered gently brushing her cheek with the back of his hand before wrapping his arms around her, he needed to be close to her he needed her to know how much he needed her.

As always his presence intoxicated her and she found herself barely able to breathe without breaking down.

'I'll be upstairs,' she said softly pushing him away still avoiding his eyes. She couldn't help the anguish she felt or the fear or what could have been and even more so, he lied to her. He kept all this hidden from _her._

'Pep, wait.' He called after her, he took a few steps forward and nearly choked on a scream, 'shit!' he yelled out, 'I thought this was healing!' he yelled up at the ceiling.

Jarvis brought up more scans, 'it is, Sir, but this still takes time.'

'Too much time,' he shouted again.

Once he finally made it up the stairs very, very slowly he came to a stop at the kitchen where he spotted a very frustrated and emotional Pepper Potts.

She was scrubbing an extremely large pot with an extraordinarily large amount of water and detergent.

'You know we have people who do that,' Tony remarked softly taking a seat at the bench, 'or at least the dishwasher.'

Pepper didn't turn to face him, 'yeah, well, I wanted to clean it.'

'You clean when you're stressed,' Tony added matter of factly.

Pepper only replied with a shrug, he really did know her too well.

She hoped that her momentary lapse in composure didn't give away too much but then again Tony was the most perceptive person when it came to these things, and right she was. Not a moment later he was standing behind her, wrapping his arms around her waist gently turning her to face him.

Water from the sink dripped haphazardly off her hands but Tony didn't care. He pulled her against him not giving her a chance to pull back this time.

'What's going on?' He asked burying his face in the nape of her neck, he knew this always got her and if it bought him some time with her he was going to play all of his cards.

He gently pushed her backwards until they were pressed up against the counter behind her while he continued to trail kisses along her neck gently pushing her hair out of the way.

Her breath hitched every time his lips made contact.

'Are you going to talk to me, or do I need to pry it out of you?' He whispered in her ear drawing another shaky breath from her lips.

'Tony stop,' she breathed already hating the words that came out of her mouth.

Secretly she thanked him for doing exactly the opposite, he gently snaked his arm to her lower back and the other weaved his fingers through her hair, 'no can do Potts, at least not until you tell me what's bothering you.'

Of course he wouldn't just give in, just like she secretly didn't want him to.

She replied by knotting her fingers through his hair and pulling him down against her, she kissed him fiercely and passionately and he replied with the same enthusiasm.

Yes she was angry that he hid this from her, but God, she didn't know what she would have done if she had known, if she'd seen him after the battle with Snow.

She needed to get that out of her mind, she held onto him with no intention of ever letting go.

His arms explored her body as they paused for a few seconds to catch their breath until Tony stopped himself abruptly noticing the stream of tears pouring from Pepper's eyes.

She tried to hide them and return to the moment but she knew as soon as he saw that, there was no more pretending, now she would have to talk, now she had no choice.

'Pepper, talk to me,' Tony said firmly taking her wrists in his hands desperately trying to get her attention.

Pepper had other ideas; she completely averted her gaze from his and focussed on keeping her composure which of course was completely impossible when her proximity to Tony was the way it was. She felt his breath so close to her she felt his eyes trying to read her, everything about him made her completely breathless.

'Pep…talk to me,' he whispered again which much more desperation in his voice now.

Finally she managed to look up and meet his eyes, worry was written all over his face but his eyes were warm, 'talk to me.' He repeated.

'You were really not going to tell me?' She whispered back.

And when the question finally made sense to Tony the warmth in his eyes was immediately replaced by darkness, he dropped his hold on her swiftly turned away.

'Tony, wait!' She called out once she found her words and her feet.

She quickly ran after him determined to resolve this.

'Tony wait!' She shouted again, this time a lot louder and this time on the main floor of their tower which also happened to be occupied by three confused Avengers.

He continued to storm down the stairs ignoring her, hurriedly walking toward his office which was ultimately Maria Hill's office.

Steve, Natasha and Bruce quickly glanced at Pepper before nodding to each other to follow.

Once he reached the door he had an audience, 'get out,' he barked at the intern who was standing beside Maria's desk working on something with her, the young man quickly gathered his things and all but ran out of the office.

Pepper swallowed hard, she had never seen such anger or darkness from Tony at least not since Aldrich. His name alone made her shudder.

Maria looked about as shocked as Pepper, the intern and the Avengers.

Tony slammed the door behind him leaving only he and Maria in the room.

'What the hell gives you the right to discuss my business with anyone?' He wasn't yelling but he wasn't keeping his voice down either. Pepper heard every word and she was certain the others had too.

In Hill's defence, she was not prepared for this but she handled it perfectly. Pepper almost smiled to herself but had to remind herself why all of this was actually happening.

'You left me no choice Tony,' she said firmly.

'I trusted you,' Tony said right back, 'to keep this kind of information safe.'

'And Miss Potts trusts you not to destroy the company you've entrusted her to look after,' she didn't back down.

Pepper could picture Tony's expression change, she definitely crossed the line.

'You had no right.' He said with the darkest undertone Pepper had ever heard from him.

'Maybe, your best interests are my job, and Miss Potts knowing, is a part of that.'

Pepper held her breath not daring to look back at the others.

Moments later the door was open and Tony stormed out leaving the five of them reeling.

She quickly remembered that Steve and Natasha knew but Bruce had no idea, she definitely didn't want to have that conversation with him.

And she knew Tony needed time. So she would leave it, at least for tonight.

* * *

 **The Day After**

Pepper awoke to an empty bed, she couldn't say she was surprised but it still hurt.

She knew he wasn't mad at her, but he couldn't face her knowing that she'd still ask the same questions and he'd have to give her the answers.

'Jarvis, where is he?' She asked swinging her legs out of bed.

'Mr Stark is currently in the workshop,' Jarvis responded.

Pepper nodded, of course he was, 'is he alone?'

'Yes Miss Potts, he's asked me to request his privacy,' he explained.

A pang of hurt shot through her, 'even from me?'

'Yes Miss Potts, but that has never stopped us before,' He said and Pepper swore he was being mischievous.

'Thank you Jarvis.' She smiled to herself.

'You're welcome Miss Potts.'

Half an hour later Pepper was showered and dressed and ready to face him, she confirmed with Jarvis that he was still there and made her way down to his work shop. True to Jarvis' word, the whole floor was empty save for the billionaire tinkering away in the corner, not even Bruce was allowed to set foot in here today.

'Thought I said not to let anyone in J,' Tony muttered keeping his eyes focussed on the screens in front of him and the broken gauntlet in his hand.

'Tony please stop this,' she said in the gentlest voice she could while walking over to him.

He actually laughed, a short, sharp sarcastic laugh. It sounded so wrong coming from him.

'Why are you taking this out on me?' Pepper finally asked dragging a stool over to him.

'No idea what you're talking about,' he muttered closing his eyes with a deep breath.

The screens in front of him instantly brought up the blueprints for the gauntlet he had in his hands and just like that endless data raced across the screen and as soon as Tony opened his eyes it stopped.

Silently he continued working; he picked up a screw driver to his left and began screwing together a loose part of the gauntlet back onto the damaged side.

'Tony,' Pepper said softly placing her hand on top of his, 'stop.'

He dropped the screw driver and pulled away from her getting to his feet.

Pepper refused to leave him, no matter what he said or how he behaved toward her. He needed her, now more than ever.

So she sat patiently watching him pace impatiently around the room until he finally stopped and leaned heavily against a bench.

He ran his hands through his hair letting out a heavy sigh.

'I'm sorry,' he started, 'I didn't mean for you to find out like that.'

'You meant for me to never find out, remember?' She reminded him gently.

'Yeah,' he smiled weakly, 'sorry about that.'

Pepper shook her head, 'I don't want an apology Tony, I just want to know why.'

She wasn't angry either, she couldn't be, especially not after everything he'd gone through, she couldn't imagine the fear and uncertainty he would have felt.

'Why I didn't tell you?' He asked, 'or why I did what I did with the Extremis?' He clarified.

Pepper shrugged, 'both.'

Tony sucked in a deep breath, 'ok…' he sighed and made his way across the room and sat back down in front of her.

'I didn't want you to talk me out of my decision…' he said finally and Pepper saw the honesty in his words.

She remained quiet; she had learned long ago that when Tony Stark needed to talk, however long it took it was something worth waiting for, being patient for.

He pinched the bridge of his nose and then took her hands in his, she could tell he was struggling with forming his explanation, after all he never thought there'd be a need to bring it up with her.

'I knew that what I was facing was a life of pain, medication, hospitals…a wheelchair…' he choked on the last word, 'and I knew that the Extremis was a possible and viable option with a very slim chance of actually working.'

Pepper swallowed the words she wanted to speak and instead squeezed his hands trying to give him strength.

'I knew that if I told you the odds you'd try to talk me out of it,' he said finally.

'Of course I would have,' Pepper agreed.

'Exactly,' he nodded, 'because you would want me alive and broken even though that's not what I want, and I know you would be the one person who would be able to talk me out of it, and I couldn't do that Pep…' he let out in almost a single breath.

Pepper finally understood and it broke her heart, 'oh Tony…' she squeezed his hands, 'I would be by your side no matter what.'

Tony nodded, 'I know, you would… maybe for the first few months, maybe years even, you'd take me to appointments, you'd sit by my side and clap while they try to rehabilitate me and maybe we'd even think we're getting somewhere…but then you wouldn't, and you'd hate yourself for thinking that and then you'd resent me, and _that_ is what I was afraid of the most.'

Pepper's jaw dropped, this was the most raw and honest thing that had ever come between them.

'It's ok Pep, doesn't make you a bad person, no one deserves a life like that, especially not you.' He got to his feet sighing.

Pepper was dumbfounded. She couldn't speak, not a word.

'That is why I did what I did,' he added smiling weakly, 'because I couldn't bear the thought of you hating yourself because of me.'

He picked up the other gauntlet and tossed it up and down in the air, clearly distracting himself from the suddenly dense air in the workshop.

A few moments passed before Pepper regained her composure and shook herself out of the shocked state she was in.

She got up and in three quick strides she had reached Tony and pulled him against her, 'I love you Tony.'

'I love you too Pep,' he murmured softly burying his face in her hair.

* * *

 **I hope the descriptions of the timing isn't too weird...I'm just trying something a little different!**

 **This will be a multi-chapter story, nothing too long, but something I felt I needed to write :)**

 **See you soon!**

 **Excelsior -SV-**


	2. Chapter 2

**Four Weeks Earlier**

SHIELD had intercepted reports of something less than ordinary only weeks after the whole mess with Maya and Aldrich was contained and cleaned up.

In that time Tony had dealt with the Extremis and ultimately fixed Pepper and himself, he finally had the arc reactor removed and felt as though his heart was actually his own once more. He didn't owe every single minute of his existence to technicalities which may or may not prove…unstable.

He knew that the Extremis wasn't safe with anyone but something deep in his core told him to hold on to it, at whatever cost.

So he had SHIELD hide it, even from him and the only person who now knew about it was Maria Hill and despite their differences he trusted her with his life, with SHIELD, which he was now the director of, and the Extremis.

So she did. She hid it out of his reach and anyone else's who may be tantalized by it.

So when this report came in Tony stood with his arms crossed staring at the familiar heat signature on the screen before him.

'How did we miss this?' He asked whoever was brave enough to answer him.

Maria stepped up, 'we didn't miss it because it didn't exist when we did all our sweeps,' she reassured him, 'I checked them myself, Tony.'

'So he had someone else out there creating this?' Tony shook his head thinking about Aldrich's ego, there was no way he would entrust his work to anyone else, 'no, this is one of the most complex bio engineered serums I've ever seen, and _believe me_ when I say there aren't many people on the planet who would know how to re-create it.'

Steve sat quietly in his chair watching the conversation unfold, already working on their plan of attack. He was the Captain of the Avengers but Stark was the Director and Steve still wanted to make sure they had covered everything before jumping in head first, as Tony often did.

He had come to respect Tony more than just a team mate and now the Director but as a friend, and with that came the territory where he could read Stark more than when they first met, which made the tell Tony was giving all the more disturbing.

Tony was trembling, to an untrained eye almost unnoticeably, but Steve wasn't untrained.

Tony was furious; a dangerous anger was building beneath the surface and shrouded amongst the raging emotions was fear.

Steve stepped up and stood beside his friend, 'what do you want to do?'

Tony shook his head and looked to Steve, 'gather the team, I only want recon for now.'

'You got it,' Steve nodded.

'We're going in tonight,' Tony added before Steve left with a nod of agreement.

Tony turned back to Maria and took over from her, 'I'll run the signatures against the ones from Rosehill, I need you to get onto Banner and see how quickly he can get here,' he kept his voice low.

'You got it Boss,' she nodded getting her phone out ready to make the call.

'Hill,' Tony said before she left, 'tell him this is potentially a Code Green.'

Maria nodded slowly pushing back the worry when she saw the concern in Tony's eyes.

Tony let out a frustrated sigh and pulled the console toward him, 'J, show me everything, side by side.'

He bowed his head leaning heavily with his arms on either side of the deck. He knew Bruce was gone, far away, and for good reason. He needed time to unwind as did they all, but he needed him, damn it if he didn't turn up he actually didn't know what to do. There wasn't a single Avenger on the team capable of dealing with what was waiting for them, except for the Hulk and maybe Thor.

But he was long gone too something about taking care of the Loki situation.

He let out a sigh and shook his head; he really was between a rock and a hard place.

'The display is up, Sir.' Jarvis announced.

'Good, let's get to work,' Tony instructed, 'and bring up my music J.'

And with that ACDC began blaring across the PA system throughout the main floor of the Avengers Tower while Tony worked tirelessly assessing the information readily available to him and breaking into secure systems to get the information which wasn't and finally comparing it all to the documents he had collected on his mission in Rosehill.

Everything was pointing in Maya's direction but none of it made sense, he pinched the bridge of his nose and closed his eyes taking a deep breath calming himself.

'What am I missing?' He muttered to Jarvis, 'there has to be something here.'

'If I may,' Jarvis began, 'Agent Hill was correct in her assessment, this is a new threat, perhaps we weren't looking in the right places.'

'So someone's framing Maya and Aldrich, why?' Tony asked looking through the digital files again.

'Perhaps it is a ruse.' Jarvis offered.

Tony hadn't considered that option; it made sense, why wouldn't someone try to play tricks on him?

He slammed his hand down against the desk, 'maybe that's what they wanted; someone to find and decipher their work.' He said finally piecing it all together in his head.

Someone like Tony who wouldn't back down knowing there was someone out there as smart or perhaps even smarter than he was.

They, whoever _they_ were, knew this would be the best tactic out there to flush him out.

Since Rosehill and Pepper and the Extremis he had been laying low, perfectly executing the entire Avenger's workload from behind the Shield.

He was pissed now.

This was the perfect way of challenging him, of trying to prove they were better than Tony Stark, and he accepted.

Tonight Rogers and Romanov would get the preliminary information he needed to at least start piecing together what they were up against.

* * *

 **The next day**

Clint dropped into one of Tony's large, leather armchairs and threw his feet up on the table in front of him much to Tony's distaste, 'what's the go Boss?'

Tony cleared his throat motioning for Clint to get his feet off the table before handing him a tablet with all the information Steve and Natasha had gathered only yesterday during a very low key, undercover recon mission.

Tony had sent them in to Aldrich's old company, Futurepharm posing as Russian scientists interested in investing which Natasha did brilliantly.

Clint gave him a smirk before taking it from him, 'recon was a success then?'

Tony nodded, 'now we know what we're up against, at least enough to to know where to start.'

Client read through the file and glanced up at Tony, 'isn't The Extremis club like some super genius only club, who are these people?'

Natasha sat quietly looking at the two men, back and forth between Clint and Tony's expressions until she caught her cue to jump in.

'As far as we knew, Tony was one of three people capable of creating something as complex as the Extremis, now it seems someone has either proven us wrong or has been sitting on this formula, waiting for their moment to shine, this suggests the latter.'

Tony almost snorted at the notion that it was even up for discussion, there was no one smart enough to do this and he was going to prove it.

'So what's the game plan then?' Clint asked taking all this information in looking up at Tony and then back at Natasha.

Tony folded his arms across his chest, 'I need to know who they are,' he said seriously, 'I need to find them, this is a direct challenge to me, they're calling me.'

'And that's exactly why you _shouldn't_ find them,' Steve added.

Tony shook his head crossing his arms, 'if they're trying to flush me out, it's working, I can't have this kind of blood on my hands,' Tony said finally.

'You're not the only one with blood on your hands, Tony, we're doing this together,' Steve added.

Tony knew he was right, this is exactly why he was here and why Steve was by his side, he knew he needed to step back and let his ego take a rest and do this the right way.

'I want everything, every bit of information you can get,' he looked at each one of the Avengers sitting before him.

Natasha nodded, 'we'll get you everything we can,' she smirked. She loved a good challenge.

Clint and Natasha took this as their cue to leave which they did silently before handing back Tony's tablet.

Tony stepped up to the consoles again and motioned for Maria to come over and handed her the tablet, 'any luck with Bruce?'

'No, I haven't been able to locate him.' She spoke quietly matching his voice.

'Ok, thanks,' he added turning back to Steve.

'Natasha would be able to-' she was cut off before she could finish.

Tony shook his head, 'no, I can't pull her out now, I need her out there…' Tony murmured, 'it's fine, we'll make do, right?' He said almost uncertainly.

She conceded, 'I'll keep trying.'

Tony thanked Maria before dismissing her but called Steve to hang back, 'I need your advice.'

He almost laughed at himself had the situation not been so serious, hell, he would have laughed even then had it not been for Steve's concerned look.

'What are we dealing with Tony?' He asked seriously folding his arms matching Tony's stance.

The two men stood silently until Tony finally spoke, 'a bit of a problem, Cap.'

'I figured that out for myself, how serious?' He asked firmly trying to gauge Tony's reactions but unfortunately for him his mask was firmly back in place and no sign of anything else could be seen in his eyes.

'I'm not worried,' Tony lied through a smirk and nonchalant shrug.

'I don't believe you,' Steve added shaking his head, refusing to believe he had imagined the sheer fleeting glimpses of terror in Tony's eyes mere moments ago.

'It's all good Cap, I promise,' he clapped him on the shoulder and turned his attention away from him trying to immediately busy himself with whatever he suddenly found interesting on the screens in front of him.

'Is that why you want Banner here?' Steve said, he didn't want to play that card, but he didn't leave him any choice.

Tony froze for a moment and then resumed doing exactly what he was doing before, distracting himself.

'That's why you're desperate to have the Hulk here, because it's nothing right, "it's all good"?'

He sucked in a deep breath and leaned heavily against the consoles, 'a precaution, that's all,' he said not turning.

'It's more than a precaution, you're worried,' Steve said matter-of-factly, he knew the man more than he let on although a lot of it was due to Tony being almost the same as Howard in these instances and a lot was just from observation. The way he would avert the conversation, hide everything in snide remarks and witty comebacks and most recently his aversion to any form of eye contact.

Finally Tony turned and looked Steve right in the eyes.

'I went up against some of the jacked up clowns Maya and Aldrich, they're bad news Cap, if this one is anything like the strongest soldier they had, we're screwed.' He explained through grit teeth, 'and from what I've read,' he pointed to the screens, 'this Snow guy is worse.'

Steve searched Tony's eyes for anything else he may be holding back, and true to Stark's nature he didn't let anything slip. His eyes were cold and calculating and suddenly Steve felt as though he was looking Howard Stark in the eyes and he was back in the forties, fighting Hydra and suddenly he knew Stark's tell. Sheer, unfiltered terror.

'Tony…' Steve began, 'what exactly are we up against?'

'Super strength, super speed, flames and anger,' Tony said flippantly, 'you know, all the stuff dreams are made of.'

Steve hardly looked amused.

'How strong are they?' Steve asked trying to drag this conversation back to where it needed to be.

'Strong,' Tony said cryptically.

Steve almost rolled his eyes, 'Tony-'

'Too strong for me, for Nat, even for you Cap.' Tony finished.

To this Steve simply replied in silence taking a moment to glance across Tony's shoulder to the screens which were playing the attacks over and over on repeat.

He looked back at the man beside him, 'what's the plan?'

Tony shrugged, 'that's where I need your advice.'

'Ok, I think we should get as much Intel about who's _running_ this show and try to stop _them_.' Steve offered.

'That's a good idea,' Tony said truthfully, 'you and Romanov head that, I don't want anyone else in on this, not until we know more.'

Steve nodded in reply, 'agreed.'

'You two need to go back in, Futurepharm has had an unexpected loss in its shares, I think the Russians need to help them along,' Tony said with a plan in mind.

'We'll head in tomorrow and see what else we can get,' Steve agreed.

'Thanks, Cap.' Tony dismissed him and turned back to the screens. 'I'll find you soon enough, wherever you're hiding.'

* * *

 **The Day the Intel Arrived….**

Tony rushed into his office, which was technically Maria Hill's now that she ran this side of things, and quickly sat down behind the large glass desk, 'show me,' he spoke to Jarvis.

'The information you requested is incomplete,' Jarvis announced.

'You didn't call me down here because you have nothing to show me, so show me,' he said impatiently.

'Indeed sir, the reports are incomplete but there are several leads which require your skills to acquire.' Jarvis offered.

Tony smirked, 'that's more like it,' he gingerly caressed the keys with his hands before his fingers brought the screens and endless streams of data to life. He typed in algorithm after algorithm setting Trojans in his wake until the back doors were soft enough to crack, once he was in he managed to override two very powerful firewalls and found exactly what he was looking for, 'got you,' he whispered with a smile.

He leaned back in his chair raising his hands from the keyboard but letting them hover, just in case.

The information they needed was right here, yes, he was definitely better than them.

This proved it.

This showed just how they had the information to formulate the Extremis.

This showed that they did in fact have a copy, albeit an unfinished copy, but what Tony didn't understand was who had completed it for them.

That would have to wait until he was face to face with the man who was foolishly trying to go toe to toe with Tony Stark.

He smirked, he was _definitely_ up for the challenge.

* * *

 **The day they met the Ghost**

Tony clenched and unclenched his fists, he watched the footage over and over again, still feeling ill every time the images of Aldrich's lab rats began to regenerate their missing limbs before finally becoming human bombs.

He flinched as the last image flashed across the screen, Pepper's Extremis transformation. The agony in her face still sent ripples of pain through him and he had to wipe away the angry tears which stung his eyes.

 _He had taken care of this, where did he go wrong?_

That was the question of the day.

He pressed his palms against the deck beside the console and pressed his face against his arm letting out a heavy sigh, he was actually scared.

He'd never encountered _anyone_ who could do what this guy did. Tony couldn't even comprehend it.

He shook his head mentally berating himself. He couldn't share this with anyone, let alone Cap and he already felt guilty about it.

If he wanted Tony, then that's what he'd give them now all he needed was a plan to get in and The Avenger's would help him.

He took every precaution to erase everything he'd found, he didn't need copies anymore he had exactly what he needed and he would never forget it.

'Jarvis, this is a direct order, do not disclose this information to anyone.' Tony said with no room for argument, 'you hear me?'

'Very well sir.' Jarvis replied.

'Good, call the team,' He called out grabbing his coat from the chair, 'tell them to head to the R and D level.'

'Contacting the Avengers now, sir.' Jarvis announced.

Tony nodded, 'oh and J, read Hill in for me, but do leave out the part about using me as bait.'

'As you wish Sir.' Jarvis agreed.

Steve was the first to arrive before Tony had even gotten there.

'By the look on your face I'm guessing you've got something?' Steve said getting up from the ledge he was perched on.

'That I do, Cap, and it's going to be one hell of a ride,' Tony said clapping his hands, 'look alive J.'

The computers surrounding them sparked to life still occasionally catching Steve off guard.

Once Natasha and Clint had joined them Tony ordered Jarvis to lock down the room and plunge it into complete radio silence.

Natasha and Clint caught on right away and made a move to switch off their cell phones encouraging Steve to do the same.

Tony's tech was absolutely impenetrable, it was one of the most sophisticated if not _the_ most sophisticated systems on the planet, everything else was corruptible.

'Ladies and Gentlemen, boys and girls,' Tony began, 'meet Ghost.'

He waved a hand in an exaggerated gesture and the screens before them all flashed to images of a man dressed in a grey, metallic suit of armour. Nothing like the Iron Man suits it was more malleable, softer, more human. He pulsated with a soft blue glow, almost shrouding him in a translucent shield of some sort.

'This is the first time anyone has been able to locate footage of this guy.' Tony added feeling proud of his achievement.

Natasha and Clint didn't even blink while Steve looked back and forth between Tony and the screens.

'Who is that?' Steve asked still trying to sound like he wasn't as shocked as he was.

Tony stuffed his hands into his pockets and turned to take in the images before him, 'he was an engineer, but now… he's a ghost,' Tony turned back to the group, 'well not the supernatural, white sheet scary type ghost,' he clarified, 'he's not quite a man and he's not quite a program, he's both.' Tony added.

Steve opened his mouth to protest and then he closed it again looking to Natasha.

'Why am I not surprised…' she added unflinchingly.

Clint shrugged and looked across at Natasha, 'ghost hunting?'

Steve still looked back at Tony perplexed, 'I'm sorry if I come across old fashioned in all this, but this sounds bad, as in if he's part of the internet and computers, how can we stop him?'

Tony smiled at him and nodded, 'fair point, that's what I'm here for, you guys do the leg work and I do the fun stuff.'

'So you know where he is?' Clint asked.

'That I do, thanks your lovely performance at Futurepharm,' he nodded to Steve and Natasha, 'he's currently housing his transparent little self in a bunker just outside the old SHIELD facility, The Cube, sound familiar?' Tony paused looking at the now shocked reactions on his team mates faces.

'I thought that was shut down,' Steve said with apparent anger.

Many unfavourable and inhumane experiments took place in The Cube and Steve knew as well as the others how bad a place it was, so the fact that it was still operational made his blood boil.

'So did I, apparently after I did a little digging,' Tony brought up another screen with reports of current experiments going on in there, 'I found a whole lota stuff I'm pretty sure they were trying really hard to hide,' he turned and grinned, 'but not hard enough it seems.'

'So what's the plan now?' Steve asked shaking his head.

'I've created a Trojan, I'll deploy it into the facility which will buy you two access to the lower floors, Steve, I want you with me-'

Steve shook his head, '-no, Tony, you're staying low on this one.'

'No can do,' Tony folded his arms across his chest.

'This isn't up for discussion-' Steve began only to be interrupted by Natasha this time.

'You can't deploy the virus remotely, can you?' She asked looking to Tony.

Tony smirked, 'that's why you're the best.'

Natasha didn't look appeased or amused or anything else for the matter. Her mask was firmly in place leaving Steve to wonder what her reaction actually was.

'In that case, Cap, you're probably the best defense Stark will have on the ground.' Clint nodded toward Tony, 'especially if we're going to have to deal with potentially freakishly modded people.'

'It's agreed then, yay.' Tony said sarcastically, 'get your things together, wheels up in ten.'

Exactly ten minutes later Tony and Steve were making their way up into the Quinjet, he didn't have the energy for pep talks or warnings or anything else the good Captain seemed to enjoy doing before they all took off on some mission or other.

This time Steve seemed to share the sentiment so instead he only made sure everyone was strapped in and ready to go.

'How far out are we?' Tony patched into the coms system and brought up Maria Hill.

'Jarvis' maps should match up to ours now, we're reading seven minutes.' She replied.

Tony re-calibrated the time with hers and Jarvis was finally up and running again.

'I do not recommend doing my system reboot on the run, Mr Stark.' Jarvis said dryly.

A chuckle left Tony's lips, 'duly noted buddy, keep an eye out, anything strikes you as strange I want you to drop connection and get out of the grid, I don't know exactly what our new friend can do, but I don't want to wait and find out, got it?'

'Of course Sir,' came the cool reply.

'You really think he can compromise Jarvis?' Natasha asked finally.

Tony nodded without dropping his gaze from the dark sky outside, 'I have no doubt that Ghost is one powerful guy,' he turned slightly and made contact with Natasha, 'and if he's managing to stay alive while commanding Snow, he's gotta have some tricks up his sleeves.'

Natasha replied with a nod and turned back to make sure they were out of earshot, content that Steve and Clint were fast asleep in the back of the jet she returned her attention to the window, 'so what's the deal, Stark, you go in and deploy the virus, wait for us to get distracted so you can go in solo?'

Tony didn't flinch, 'no idea what you're talking about Romanov.'

'I hope you know what you're doing.' She said instead.

 _So do I,_ Tony thought to himself.

'Two minutes until touch down.' Jarvis announced rising Steve and Clint from their sleep.

'Get your gear ready,' Tony said with a deep breath, 'we have one shot at this.'

Everyone silently nodded making sure each knew their position.

'Thirty seconds until touch down.' Jarvis announced.

Tony called on his armour while Steve gripped his shield and Clint and Natasha readied their weapons.

'Stay in contact team, 'Tony shouted as the jet touched down and the door opened letting in a rush of wind into the jet.

They disappeared into the darkness taking their posts just as they had discussed while Tony took off into the night letting Jarvis run full perimeter scans.

'Keep an eye out for Extremis heat signatures,' Tony said soaring high above the compound, 'we have no idea what else they've been cooking up in there.'

'The scans so far show nothing out of the ordinary,' Jarvis said, 'the compound is completely abandoned.'

Tony looked through the scans showing up on the HUD, 'there's something out of place here, J, doesn't it seem off?'

'Perhaps the underground bunkers may be worth looking at?' Jarvis offered.

'Absolutely, all those freaks we saw haven't just disappeared,' Tony dropped altitude in a fast, determined free fall coming just short of the concrete slabs surrounding the grounds, 'all you J.'

Jarvis brought up infrared scans once again and this time Tony spotted just what he was looking for.

'I found where our guest is hiding the party,' Tony spoke into the coms.

'You and I still have a very different definition of _party_.' Natasha replied dryly.

Tony's laugh echoed through the coms, 'just make your way over.'

'I actually kinda like Tony's parties,' Clint trailed off jumping down from a second floor roof he'd just gotten comfortable on.

'Speak for yourself,' Steve chimed in, 'I like going to a party without the risk of getting blown up, just saying.'

'Wow, was that a joke?' Tony asked incredulously landing precisely at his chosen location.

Clint snorted his response while Natasha smirked to herself, 'let's just focus on the task at hand boys,' she grinned.

Steve finally reached Tony's location and stored his shield, 'what's down there?'

'At least twenty heat signatures,' Tony spoke as Natasha and Clint arrived, he raised the face plate, 'from what I can see only one is infected with the Extremis and I'm guessing that's Snow, the others are human.'

'Sounds like a good party,' Clint mused to which Tony choked back a laugh.

'Where's the server room?' Natasha asked folding her arms across her chest ignoring the two men, they were far too alike.

Tony brought up a holographic image of the structure beneath the surface and zoomed in to a room about twenty yards away, 'right here.'

'So we need to get to that room first,' Clint looked to Natasha, 'Nat and I will cover you.'

Tony nodded dropping the face plate, 'Cap, we're up.'

Steve took the lead flanking Tony while he cracked the electronic lock to the compound and once they were in Tony stepped out of his armour and lead Steve down the hall.

He readied his shield in case anything unexpected came their way since his main job now was making sure Tony reached the Server Room without incident.

Through the coms they heard Natasha and Clint making headway taking out the stray guards who were lazily guarding an abandoned building, Tony could have laughed had the situation not been so trying.

'Think Ghost will make an appearance?' Steve whispered to Tony as they made their way down the winding corridors.

Tony replied with a quick shrug, 'who knows, anything's possible.'

Steve and Tony finally reached their destination and Steve took guard by the door while Tony knelt down in front of the electronic lock.

'Hello there beautiful,' Tony said softly taking out a small electro magnet he obviously had hidden in his pockets all along.

'Is that safe?' Steve asked quietly looking back at Tony over his shoulder.

'Sure it is,' Tony replied softly, 'you might want to get that shield ready.'

'What?' Steve asked quickly, 'why?'

Before he could get his response Tony pressed the electro magnet to the lock and in one quick, violent bang the lock blew off the door sending Tony stammering backwards and Steve readying himself for the onslaught of guards which he knew would be rushing down any minute.

'You could have warned me!' Steve hissed keeping his eyes open.

Tony grinned getting to his feet, 'I did,' he added before pushing the smoking door open and slipping inside.

Just outside Tony heard Steve battling it out with at least a dozen guards while he worked quickly to deploy the Trojan horse.

'Bring em' home,' he smirked to himself and just as he was about to hit Enter, a blue, blinding light pulsed through the servers and into Tony.

He dropped to his knees with sharp gasp, 'what the hell…' his first thought was that he had electrocuted himself, he'd done it so many times when he was tinkering he definitely recognised the feeling. He also went through that kind of torture in Afghanistan while they burned his reactor while they were drowning him in the water troughs.

The hazy pain which quickly built in intensity reverberated through his body and suddenly any movement he tried to make was excruciating, he squeezed his eyes shut focusing solely on breathing while working out what his next move would be.

'Tony Stark….' He heard the voice as though it was inside his skull along with a thousand needles and electric pokers.

He let out a painful breath and looked up through watery eyes, 'Ghost…' he managed.

'I see your reputation precedes you.' The mechanical voice spoke again.

Tony grit his teeth since speaking was pointless, he couldn't form a single coherent thought in his head let alone speak it aloud.

'Your plan almost worked,' the Ghost spoke, 'but you didn't count on one, small thing.'

Tony grimaced again as the pulsing pain shot through him, he then realised that he was shocking him with pulses of electricity and electricity connected Ghost to the servers and the servers were connected to everything.

Ghost stepped toward him and knelt down pressing one of his palms against Tony's wrist sending shockwaves through him, 'you didn't take into account the fact that I am smarter than you.'

Tony clenched his fists mustering up every single ounce of strength he could, gritting his teeth he lunged forward and slammed his palm on the keyboard and hit Enter.

The only thing louder and more painful in his head than his own scream was the guttural noise which came from Ghost and as quickly as he had appeared he was gone, 'God that was awful,' Tony mused rubbing the sore spot in his wrist where Ghost's touch had left electrical burns.

Tony leaned his weight on his knee resting his elbow on his leg, 'everyone ok?' he breathed into his coms as soon as he could speak.

'Yeah, we're fine, what the hell was that?' Clint replied equally as confused as Tony.

Steve came rushing through the door and down beside Tony, 'you alright?' He asked helping the billionaire to his feet.

Tony took a moment to steady himself on his feet and catch his breath, 'yeah, I think our guest is pissed we crashed the party.'

'What happened?' Natasha asked quickly rounding the corner.

Tony turned back to the servers finally being able to stand on his feet without feeling the need to vomit, 'he was a little pissed that I tried to infect him.'

'Did you manage to get it done?' Clint asked to which Tony replied with a snort.

'Of course I did,' he discretely glanced down at his hands, damn, he was still shaking and the burn was violently contrasting the tanned skin on his arms, 'wasn't easy but I did.'

'You should get checked out,' Steve said storing his shield, 'we've done all we can tonight.'

'Agreed,' Tony muttered.

He still couldn't shake the feeling in his head and the way his body felt as though it was on fire from the inside out, having someone inside you, completely filling you.

It wasn't something Tony was used to, his body shivered involuntarily and he instinctively wrapped his arms around himself to keep warm.

Steve fell back and motioned for Clint to help Tony to the jet, 'Natasha, keep an eye on him, I don't know much about this kind of stuff, but the current running through that room was off the charts, Tony took the hit head on.'

'I know,' she nodded, 'I saw the readings when I walked in.' Natasha used electric currents built into her suit; she always had to keep accurate readings to prevent things like short circuiting and current failure especially when she counted on them during a fight. So it was no surprise that she had equipment which could read the charge in the room.

That made her all the more worried about Tony's wellbeing, he wasn't himself.

He was closed off in a room in which an electric current of more than ten thousand volts was contained with him in it with no protective gear.

How he was still alive was a complete mystery to her.

The Avengers took off, flying in to the night away from the danger in The Cube. Tony sat with his knees against his chest shaking violently as his heart still tried to catch up to its own rhythm.

Natasha turned back to look at him every so often but never actually spoke, she knew the look in his eyes and quite frankly it worried her. She recognised the determination and sheer will to hold it together despite the agony she imagined he was going through.

Her quick glances back every few minutes or so cemented that, his knuckles were white from gripping his jeans so tightly. His face was completely emotionless as his jaw clenched and unclenched every so often letting out only a barely audible whimper.

On the surface he was still but behind his eyes she saw the pain raging and washing through him.

She turned back to the console and let out a quiet breath.

'Jarvis, are you there?' She asked bringing up the last dialled call.

The jet remained silent, Jarvis had bailed, just as Tony had advised him to.

She manually pressed the dial button and waited for Maria's face to populate the screen.

'I heard you took a hit,' she murmured as soon as she was connected to the Quinjet's com systems.

Her expression was as sullen as the mood on the jet was.

No one had spoken since Tony collapsed against the back of the jet and curled up and away from the world into his own catatonic state.

Steve nodded to the Agent, 'it was bad.'

'We'll walk it off, we always do,' Clint added bowing his head.

The rest of the flight was silent save for the occasional whimper from Tony and the nervous sigh from Steve and it did little to quiet Natasha's own demons.

Her eyes fell on the darkness outside and the familiar safety it brought her, she was determined now, almost as much as Tony was that this needed to be sorted out.

* * *

 **So another chapter down, I think I forgot to mention that this is loosely based on The Invincible Iron Man - Dark Reign as well as a few other comics I've read along the way.**

 **Hope that makes sense :)**

 **Enjoy!**


End file.
